The skimmer has a weir door that pivots and floats. This is what causes the skimming action that draws floating debris across your pond and into the skimmer basket. When a fish accidently gets drawn in, it can't escape and gets trapped in the basket. They are generally fine in there as long as you are checking your skimmer basket every couple of days.
One easy fix you can do, is to use a rock to weigh the weir door down. This allows fish and other aquatic life to swim into the skimmer and back out, but it will not draw floating debris as effectively into the skimmer basket.
I use a rock on my weir door when the pond has tadpoles and remove the rock to allow better skimming action when trees are dropping seeds in the spring and leaves in the fall. I, also, keep the weir up over the winter.